# NCLEdetector Public Datastore Release v1.0.0

This is the public release of the NCLEdetector datastore containing example outputs and reference data for all four workflows.

## Contents

### user_input.tar.gz
Reference structures, experimental data, and benchmark datasets:
- Reference protein structures (PDB format)
- Experimental LiP-MS and XL-MS data
- Secondary structure definitions
- Benchmark test cases

### Per-Analysis Archives (workflow1-4/)
Individual analysis outputs compressed for efficient download:

**Workflow 1 (Native NCLE Detection):**
- `workflow1_NCLE.tar.gz` — Native entanglement detection output
- `workflow1_HQ_NCLE.tar.gz` — High-quality NCLE filtering results
- `workflow1_clustered_HQ_NCLE.tar.gz` — Clustered NCLE results
- `workflow1_clustered_HQ_NCLE_features.tar.gz` — Feature calculations

**Workflow 2 (Trajectory Analysis):**
- `workflow2_OP.tar.gz` — Order parameters (Q, G, K, SASA, XP)
- `workflow2_OP_last335.tar.gz` — OP analysis on trailing 335 frames
- `workflow2_OP_AA_last335.tar.gz` — All-atom OP calculations
- `workflow2_MSM.tar.gz` — Markov State Model
- `workflow2_MSMStats*.tar.gz` — MSM statistics and folding pathways
- `workflow2_FoldingPathway*.tar.gz` — Folding pathway analysis
- `workflow2_nonnative_clustering_last335.tar.gz` — Non-native entanglement clustering

**Workflow 3 (Sim-to-Experiment Consistency):**
- `workflow3_MassSpec_ConsistencyTest.tar.gz` — LiP-MS/XL-MS consistency test results

**Workflow 4 (Population Modeling):**
- `workflow4_monte_carlo.tar.gz` — Monte Carlo simulations
- `workflow4_population_modeling.tar.gz` — Population-level statistics
- `workflow4_nativeNCLE_all.tar.gz` — Batch native NCLE analysis

## Release Information

- **Version:** 1.0.0
- **Release Date:** 2026-07-26
- **Software Version:** NCLEdetector 1.1.6
- **Git Commit:** 32096314b8940f7583b5f02ae817025bc2b4f1de
- **Total Size:** ~500 GB (archives only)
- **File Count:** 59,546 files

## Download Instructions

### Using curl (individual files)
```bash
curl -O https://downloads.ncleweb.org/NCLEdetector_Datastore/v1.0.0/user_input.tar.gz
curl -O https://downloads.ncleweb.org/NCLEdetector_Datastore/v1.0.0/outputs/workflow2/workflow2_OP.tar.gz
```

### Using rclone (bulk download)
Configure rclone for HTTPS and then:
```bash
rclone copy \
  https://downloads.ncleweb.org/NCLEdetector_Datastore/v1.0.0/ \
  /local/download/path/ \
  --progress
```

## Verification

All archives have been validated for integrity. To verify checksums:

```bash
sha256sum -c SHA256SUMS
```

## Citation

If you use this dataset in your research, please cite:

```
@dataset{ncledetector_public_2026,
  title={NCLEdetector Public Datastore v1.0.0},
  author={O'Brien Lab},
  year={2026},
  month={July},
  doi={10.xxxx/zenodo.xxxxxxx},
  url={https://downloads.ncleweb.org/NCLEdetector_Datastore/v1.0.0/}
}
```

See CITATION.cff for additional citation formats.

## License

See LICENSE file. This dataset is released under [LICENSE TYPE].

## Support

For issues or questions about this dataset, contact: [contact information]

## Additional Resources

- Full software documentation: https://ncleweb.org/docs
- Tutorial workflows: https://ncleweb.org/tutorials
- Source code: https://github.com/[repo]